{"id":"W2150856587","doi":"10.1093/bioinformatics/bth057","title":"Cluster Analyzer for Transcription Sites (CATS): a C++-based program for identifying clustered transcription factor binding sites","year":2004,"lang":"en","type":"article","venue":"Bioinformatics","topic":"Genomics and Chromatin Dynamics","field":"Biochemistry, Genetics and Molecular Biology","cited_by":9,"is_retracted":false,"has_abstract":true,"ca_institutions":"D-Wave Systems (Canada)","funders":"Howard Hughes Medical Institute","keywords":"Transcription factor; DNA binding site; Consensus sequence; Biology; Computational biology; Transcription (linguistics); Genome; Binding site; CATS; DNA; Genetics; DNA sequencing; Gene; Promoter; Computer science; Base sequence; Gene expression","routes":{"ca_aff":true,"ca_fund":false,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"metacan-v3-hybrid-931329e0061c","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.002807275,0.003193524,0.001665781,0.002690125,0.001176549,0.001689597,0.003849373,0.0009653245,0.04301214],"category_scores_gemma":[0.004407361,0.001490018,0.001518648,0.002151367,0.0007266378,0.001677301,0.00145202,0.003120845,0.0240014],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.001001571,"about_ca_system_score_gemma":0.00201069,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.003397576,"about_ca_topic_score_gemma":0.003740925,"domain_scores_codex":[0.9989737,0.0001742515,0.0001237057,0.0003202794,0.000309724,0.00009829382],"domain_scores_gemma":[0.9982221,0.0008954777,0.0002006014,0.0001467133,0.0003879388,0.0001471555],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"not_applicable","study_design_gemma":"simulation_or_modeling","study_design_scores_codex":[0.003854763,0.0003914607,0.006249014,0.004109397,0.0006497249,0.000911689,0.001060218,0.01707024,0.07808197,0.01262949,0.574352,0.30064],"study_design_scores_gemma":[0.00201119,0.0006759802,0.01112445,0.0006157224,0.0004202724,0.00167837,0.0003518359,0.3967449,0.1336663,0.04368518,0.4084252,0.000600643],"study_design_candidate":"simulation_or_modeling","study_design_consensus":null,"genre_codex":"methods","genre_gemma":"software","genre_scores_codex":[0.006029956,0.000331751,0.5883443,0.000230525,0.0001855207,0.0009197426,0.032327,0.367636,0.003995128],"genre_scores_gemma":[0.02164316,0.0003076931,0.8948964,0.0002630565,0.00006929469,0.002671524,0.04335851,0.03159762,0.005192794],"genre_candidate":"software","genre_consensus":null,"teacher_disagreement_score":0.04301214,"threshold_uncertainty_score":0.14389,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.03079255120416373,"score_gpt":0.2834839935097028,"score_spread":0.2526914423055391,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}